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<div class="header">
  <div class="summary">
<a href="#nested-classes">Classes</a> &#124;
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<p>Base docs for the cudamapper package (tbd)  
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Classes</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">claragenomics::cudamapper::Index</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html" title="Index - manages mapping of (k,w)-kmer-representation and all its occurences.">Index</a> - manages mapping of (k,w)-kmer-representation and all its occurences.  <a href="classclaragenomics_1_1cudamapper_1_1Index.html#details">More...</a><br /></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html">claragenomics::cudamapper::Matcher</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Matcher.html" title="Matcher - base matcher.">Matcher</a> - base matcher.  <a href="classclaragenomics_1_1cudamapper_1_1Matcher.html#details">More...</a><br /></td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">claragenomics::cudamapper::Overlapper</a></td></tr>
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<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html">claragenomics::cudamapper::Sequence</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classclaragenomics_1_1cudamapper_1_1Sequence.html" title="Sequence - represents an individual read (name, DNA nucleotides etc)">Sequence</a> - represents an individual read (name, DNA nucleotides etc)  <a href="classclaragenomics_1_1cudamapper_1_1Sequence.html#details">More...</a><br /></td></tr>
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<tr class="memdesc:"><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html" title="SketchElement - Contains integer representation, position, direction and read id of a kmer.">SketchElement</a> - Contains integer representation, position, direction and read id of a kmer.  <a href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#details">More...</a><br /></td></tr>
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="func-members"></a>
Functions</h2></td></tr>
<tr class="memitem:ga569c8855bdf9806d3747b26fc7e98975"><td class="memItemLeft" align="right" valign="top"><a id="ga569c8855bdf9806d3747b26fc7e98975"></a>
virtual&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudamapper.html#ga569c8855bdf9806d3747b26fc7e98975">claragenomics::cudamapper::Overlapper::~Overlapper</a> ()=default</td></tr>
<tr class="memdesc:ga569c8855bdf9806d3747b26fc7e98975"><td class="mdescLeft">&#160;</td><td class="mdescRight">Virtual destructor for <a class="el" href="classclaragenomics_1_1cudamapper_1_1Overlapper.html">Overlapper</a>. <br /></td></tr>
<tr class="separator:ga569c8855bdf9806d3747b26fc7e98975"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:gab0e3be4a9442dfb2b7952fb473e591a3"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudamapper.html#gab0e3be4a9442dfb2b7952fb473e591a3">claragenomics::cudamapper::Overlapper::get_overlaps</a> (std::vector&lt; <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a> &gt; &amp;overlaps, thrust::device_vector&lt; <a class="el" href="structclaragenomics_1_1cudamapper_1_1Anchor.html">Anchor</a> &gt; &amp;anchors, const <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> &amp;index_query, const <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> &amp;index_target)=0</td></tr>
<tr class="memdesc:gab0e3be4a9442dfb2b7952fb473e591a3"><td class="mdescLeft">&#160;</td><td class="mdescRight">returns overlaps for a set of reads  <a href="group__cudamapper.html#gab0e3be4a9442dfb2b7952fb473e591a3">More...</a><br /></td></tr>
<tr class="separator:gab0e3be4a9442dfb2b7952fb473e591a3"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga54fedd97206ad1691f7b9d9966d01371"><td class="memItemLeft" align="right" valign="top"><a id="ga54fedd97206ad1691f7b9d9966d01371"></a>
static void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudamapper.html#ga54fedd97206ad1691f7b9d9966d01371">claragenomics::cudamapper::Overlapper::print_paf</a> (const std::vector&lt; <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a> &gt; &amp;overlaps)</td></tr>
<tr class="memdesc:ga54fedd97206ad1691f7b9d9966d01371"><td class="mdescLeft">&#160;</td><td class="mdescRight">prints overlaps to stdout in <a href="https://github.com/lh3/miniasm/blob/master/PAF.md">PAF format</a> <br /></td></tr>
<tr class="separator:ga54fedd97206ad1691f7b9d9966d01371"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ga3e5732f34489315ec8d1ef8b82ccea5c"><td class="memItemLeft" align="right" valign="top">static void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="group__cudamapper.html#ga3e5732f34489315ec8d1ef8b82ccea5c">claragenomics::cudamapper::Overlapper::filter_overlaps</a> (std::vector&lt; <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a> &gt; &amp;filtered_overlaps, const std::vector&lt; <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a> &gt; &amp;overlaps, size_t min_residues=5, size_t min_overlap_len=0)</td></tr>
<tr class="memdesc:ga3e5732f34489315ec8d1ef8b82ccea5c"><td class="mdescLeft">&#160;</td><td class="mdescRight">removes overlaps which are unlikely to be true overlaps  <a href="group__cudamapper.html#ga3e5732f34489315ec8d1ef8b82ccea5c">More...</a><br /></td></tr>
<tr class="separator:ga3e5732f34489315ec8d1ef8b82ccea5c"><td class="memSeparator" colspan="2">&#160;</td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<p>Base docs for the cudamapper package (tbd) </p>
<h2 class="groupheader">Function Documentation</h2>
<a id="ga3e5732f34489315ec8d1ef8b82ccea5c"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ga3e5732f34489315ec8d1ef8b82ccea5c">&#9670;&nbsp;</a></span>filter_overlaps()</h2>

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          <td class="memname">static void claragenomics::cudamapper::Overlapper::filter_overlaps </td>
          <td>(</td>
          <td class="paramtype">std::vector&lt; <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a> &gt; &amp;&#160;</td>
          <td class="paramname"><em>filtered_overlaps</em>, </td>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const std::vector&lt; <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a> &gt; &amp;&#160;</td>
          <td class="paramname"><em>overlaps</em>, </td>
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          <td class="paramkey"></td>
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          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>min_residues</em> = <code>5</code>, </td>
        </tr>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>min_overlap_len</em> = <code>0</code>&#160;</td>
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          <td>)</td>
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<p>removes overlaps which are unlikely to be true overlaps </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">filtered_overlaps</td><td>Output vector in which to place filtered overlaps </td></tr>
    <tr><td class="paramname">overlaps</td><td>vector of <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a> objects to be filtered </td></tr>
    <tr><td class="paramname">min_residues</td><td>smallest number of residues (anchors) for an overlap to be accepted </td></tr>
    <tr><td class="paramname">min_overlap_len</td><td>the smallest overlap distance which is accepted </td></tr>
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<a id="gab0e3be4a9442dfb2b7952fb473e591a3"></a>
<h2 class="memtitle"><span class="permalink"><a href="#gab0e3be4a9442dfb2b7952fb473e591a3">&#9670;&nbsp;</a></span>get_overlaps()</h2>

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          <td class="memname">virtual void claragenomics::cudamapper::Overlapper::get_overlaps </td>
          <td>(</td>
          <td class="paramtype">std::vector&lt; <a class="el" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a> &gt; &amp;&#160;</td>
          <td class="paramname"><em>overlaps</em>, </td>
        </tr>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">thrust::device_vector&lt; <a class="el" href="structclaragenomics_1_1cudamapper_1_1Anchor.html">Anchor</a> &gt; &amp;&#160;</td>
          <td class="paramname"><em>anchors</em>, </td>
        </tr>
        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> &amp;&#160;</td>
          <td class="paramname"><em>index_query</em>, </td>
        </tr>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const <a class="el" href="classclaragenomics_1_1cudamapper_1_1Index.html">Index</a> &amp;&#160;</td>
          <td class="paramname"><em>index_target</em>&#160;</td>
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          <td>)</td>
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<span class="mlabels"><span class="mlabel">pure virtual</span></span>  </td>
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<p>returns overlaps for a set of reads </p>
<dl class="params"><dt>Parameters</dt><dd>
  <table class="params">
    <tr><td class="paramname">overlaps</td><td>Output vector into which generated overlaps will be placed </td></tr>
    <tr><td class="paramname">anchors</td><td>vector of anchor objects. Does not need to be ordered </td></tr>
    <tr><td class="paramname">index_query</td><td>representation index for reads </td></tr>
    <tr><td class="paramname">index_target</td><td></td></tr>
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